7P35

Structure of the SARS-CoV-2 3CL protease in complex with rupintrivir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherSARS-CoV-2 3CL protease

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293Triammonium citrate, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0339.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.023α = 90
b = 54.024β = 100.774
c = 114.067γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M2020-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25656.09184.40.9989.62.521599
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2562.2950.58

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUESARS-CoV-2 3CL protease2.25656.09121599111584.3880.2030.20.258150.928
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.0470.022-0.034-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_dihedral_angle_4_deg19.495
r_dihedral_angle_other_3_deg17.903
r_dihedral_angle_3_deg16.103
r_lrange_it9.868
r_lrange_other9.867
r_dihedral_angle_1_deg8.117
r_scangle_it6.215
r_scangle_other6.214
r_mcangle_it5.511
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_dihedral_angle_4_deg19.495
r_dihedral_angle_other_3_deg17.903
r_dihedral_angle_3_deg16.103
r_lrange_it9.868
r_lrange_other9.867
r_dihedral_angle_1_deg8.117
r_scangle_it6.215
r_scangle_other6.214
r_mcangle_it5.511
r_mcangle_other5.511
r_scbond_it4.06
r_scbond_other4.059
r_mcbond_it3.643
r_mcbond_other3.638
r_angle_refined_deg1.471
r_angle_other_deg1.222
r_nbd_other0.212
r_nbd_refined0.204
r_symmetry_nbd_other0.195
r_symmetry_nbd_refined0.184
r_symmetry_xyhbond_nbd_refined0.18
r_nbtor_refined0.162
r_xyhbond_nbd_refined0.129
r_symmetry_nbtor_other0.079
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4694
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing